A child born to a foreign couple in Japan who does not have Japanese nationality but intends to reside in Japan must apply within 30 days after birth for a status of residence at the immigration bureau for its district.
However, if the child will leave the country within 60 days this is not necessary.
Even if a passport has not been obtained, an application should be made.

Note 1 The information given is that confirmed as of July 2002. Note that a new system or system revisions may have been introduced after this date.

This information is from the CLAIR website. The Council of Local Authorities for International Relations (CLAIR) was established in July 1988 in response to rising concerns about local level internationalization in Japan.